rs104886161
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP3_ModeratePP5_Moderate
The NM_033380.3(COL4A5):c.2146G>A(p.Gly716Ser) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. G716G) has been classified as Likely benign.
Frequency
Consequence
NM_033380.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A5 | NM_033380.3 | c.2146G>A | p.Gly716Ser | missense_variant, splice_region_variant | 27/53 | ENST00000328300.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A5 | ENST00000328300.11 | c.2146G>A | p.Gly716Ser | missense_variant, splice_region_variant | 27/53 | 1 | NM_033380.3 | ||
COL4A5 | ENST00000483338.1 | c.970G>A | p.Gly324Ser | missense_variant, splice_region_variant | 11/20 | 1 | |||
COL4A5 | ENST00000361603.7 | c.2146G>A | p.Gly716Ser | missense_variant, splice_region_variant | 27/51 | 2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 917930Hom.: 0 Cov.: 17 AF XY: 0.00 AC XY: 0AN XY: 245198
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
X-linked Alport syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | research | Precision Medicine Center, Zhengzhou University | - | PVS1:Null variant in the gene with established LOF as a disease mechanism PM2:not found in gnomAD PP3:Multiple lines of computational evidence support a deleterious effect on the gene or gene product - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.